Contacts of the helix formed by residues 267 - 279 (chain B) in PDB entry 2IBN
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 267 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B PHE* 4.0 29.2 - - + -
104B GLU* 3.7 45.8 - - + +
107B ARG* 4.2 9.4 - - - +
264B VAL* 3.1 34.2 + - + +
266B LYS* 1.3 79.4 - - + +
268B ARG* 1.3 65.0 + - - +
269B PRO* 3.4 0.4 - - - -
270B TYR* 3.1 17.0 + - - +
271B TYR* 3.2 20.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MSE 3.4 33.5 - - + +
78B ASP* 2.8 42.8 + - - -
100B PHE* 4.0 21.3 - - + -
264B VAL 3.6 10.8 - - - +
265B ASP* 3.3 33.4 + - - +
267B LEU* 1.3 76.1 - - - +
269B PRO* 1.3 70.2 - - + +
271B TYR 3.3 0.7 + - - -
272B GLN* 2.9 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 269 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ASP 3.3 15.5 - - - +
266B LYS* 3.5 13.7 - - - +
267B LEU 3.5 0.4 - - - -
268B ARG* 1.3 91.0 - - + +
270B TYR* 1.3 62.5 + - - +
272B GLN* 3.7 7.4 - - + +
273B GLY* 3.1 18.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 270 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ARG* 3.5 48.0 - - - +
114B ASP* 3.8 7.7 - - + +
117B HIS* 2.6 30.9 + - - -
266B LYS 5.0 1.5 + - - +
267B LEU* 3.1 11.2 + - - +
269B PRO* 1.3 79.9 - - - +
271B TYR* 1.3 80.5 + + - +
273B GLY* 3.1 11.6 + - - -
274B LEU* 3.3 45.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 271 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MSE 4.2 8.5 - - + -
100B PHE* 3.9 21.3 - + + -
103B ALA* 3.3 39.8 + - + +
104B GLU* 2.6 30.9 + - + -
107B ARG* 4.0 5.6 + - - -
117B HIS* 4.1 9.6 - - + +
118B LEU* 4.9 1.5 - - + +
121B LEU* 4.0 29.8 - - + -
267B LEU* 3.2 32.8 + - + +
268B ARG 4.2 1.8 - - - +
270B TYR* 1.3 93.5 - + - +
272B GLN* 1.3 60.3 + - - +
274B LEU* 3.2 22.4 + - + +
275B ILE* 2.9 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 272 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MSE 3.6 38.1 + - + +
268B ARG* 2.9 31.1 + - + +
269B PRO* 3.7 7.0 - - + +
271B TYR* 1.3 75.7 - - - +
273B GLY* 1.3 57.2 + - - +
275B ILE* 3.4 20.4 + - - +
276B ASP* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PRO 3.1 9.7 + - - -
270B TYR 3.1 10.1 + - - -
272B GLN* 1.3 76.1 - - - +
274B LEU* 1.3 58.3 + - - +
276B ASP* 3.4 10.0 + - - +
277B LYS* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.4 53.4 - - + +
117B HIS* 3.9 9.2 - - + -
118B LEU* 4.0 20.0 - - + +
270B TYR* 3.3 49.2 + - + +
271B TYR* 3.2 17.8 + - + +
273B GLY* 1.3 74.2 - - - +
275B ILE* 1.3 61.8 + - - +
277B LYS* 3.1 8.7 + - + +
278B TYR* 2.9 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 275 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B THR* 6.0 1.8 - - - -
73B VAL* 3.6 43.1 - - + +
74B MSE 4.3 12.8 - - + +
118B LEU* 4.2 12.6 - - + -
121B LEU* 4.1 10.8 - - + -
271B TYR 2.9 24.6 + - - +
272B GLN* 3.6 24.7 - - - +
274B LEU* 1.3 75.9 - - - +
276B ASP* 1.3 56.2 + - - +
279B CYS* 2.9 59.7 + - - +
280B PRO* 4.5 4.5 - - + -
281B GLY 5.1 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 276 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B GLN 3.0 17.1 + - - +
273B GLY* 3.4 10.5 - - - +
274B LEU 3.3 0.2 - - - -
275B ILE* 1.3 75.9 - - - +
277B LYS* 1.3 62.7 + - - +
280B PRO* 3.4 32.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 3.1 29.2 + - - +
208B SER* 3.8 6.9 + - - -
273B GLY 3.1 13.7 + - - +
274B LEU* 3.1 12.0 + - + +
276B ASP* 1.3 80.9 - - - +
278B TYR* 1.3 91.0 + - + +
280B PRO* 4.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASP* 2.6 41.4 + - - -
115B TRP* 3.6 27.5 - - + +
118B LEU* 3.6 26.7 - - + -
206B LYS 4.7 0.5 - - - +
207B PHE* 3.6 2.9 - - - +
208B SER* 2.9 59.5 + - - +
209B LEU* 3.8 14.4 - - + -
210B PRO* 5.7 0.9 - - + -
274B LEU* 2.9 22.2 + - + -
277B LYS* 1.3 106.7 + - + +
279B CYS* 1.3 63.4 + - - +
280B PRO* 3.9 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 279 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 3.7 19.7 - - - +
118B LEU* 4.0 22.0 - - - -
122B LEU* 4.4 2.7 - - - -
205B ASN 6.2 0.2 - - - -
207B PHE* 3.6 42.0 - - + +
275B ILE* 2.9 31.3 + - - +
278B TYR* 1.3 82.4 - - - +
280B PRO* 1.3 69.8 - - - +
281B GLY 4.5 0.7 - - - +
283B LEU* 4.0 14.5 - - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il